Bring a large pot of salted water to a boil. Add pasta; cook until barely tender, about 8 minutes, then add zucchini. Cook until pasta is al dente and zucchini barely tender, about 3 minutes (it will continue to cook off the heat). Drain, reserving 1/2 cup pasta water.
Meanwhile, put oil, cumin, lime zest, garlic, salt, and 1/2 cup pepitas in a blender and blend until smooth. Add 2 cups cilantro; process just until smooth, about 15 seconds. Pour into a bowl and stir in lime juice, chile flakes, and 1/2 cup cotija.
Return pasta and zucchini to warm pot. Toss with cilantro pesto and pour in enough pasta water to loosen. Divide among 4 wide bowls, then sprinkle with remaining cotija, cilantro, and pepitas.